A system and method protect a thruster assembly disposed with a pontoon of a semi-submersible drilling vessel during dry tow transport. A cover may be positioned over the thruster assembly and secured with the pontoon. A thruster cover support structure may be disposed with the pontoon. The thruster cover support structure may be a frame positioned around the pontoon for removable attachment with the thruster cover. The thruster cover support structure may be a bracket, ring or flange fixedly attached with the pontoon. The thruster cover may be removably disposed with the bracket, ring or flange, such as by bolting or welding. A spacer barge may be positioned below the pontoon between thruster assemblies for lifting the semi-submersible drilling vessel before placement of the spacer barge and semi-submersible vessel on the dry tow transporting vessel. The thruster assemblies may be elevated and in some embodiments positioned directly over the dry tow transporting vessel.